Yes. ClickGUARD's Google Ads tracking template works with parallel tracking. The only difference between using parallel tracking and the previous model is that ClickGUARD no longer forwards visitors to your landing pages as a proxy, but rather logs and processes information about the click in the background.
What is parallel tracking?
Parallel tracking in Google reduces the time it takes a visitor to reach your landing pages after clicking on your ads. The way this is achieved is by sending the visitor to your landing page directly to your final URL while the tracking (click measurement) happens in the background, in parallel.
After October 30th, 2018 parallel tracking became required for all advertisers using third-party click measurement systems.
You can read more about how parallel tracking works here.
Are there any issues with custom tracking templates?
Even if you're using custom tracking templates on account (or lower) level ClickGUARD's tracking will not be affected by parallel tracking, as long as you used ClickGUARD's template merge tool.
Best approach is to remove lower-than-account level tracking templates and move the custom URL parameters into the final URL suffix setting.